Hey guys well let me tell you my story. I have an '06 mustang which was involved in an accident...some girl smashed into my right side as i was passing her on the side and totally destroyed the right side fender and scratched the car all the way to the back...

My Doors were locking perfectly before and after the accident with the remote. One press would lock and two presses would beep the horn and flash the lights real quick. Here is where the thing gets messed up. I dropped off my car at a body shop to get repaired and after about a week I got the car back looking perfect.

I get home, park the car and when I am about to leave the car I hit the remote twice to lock the doors and hear the beep like I am used to hearing... Instead I get this: the doors lock and I get 2 beeps and my lights don't flash... wtf? I am not sure if the locking anti theft is working correctly anymore? would disconnecting the battery for a long period of time mess that up? would it need reprogramming? I am just concerned because I get no indication the doors are actually locked...I have to physically check them both now everytime its driving me crazy... I hope someone can chime in please. Thx

I forgot and left my truck ajar last week, I had hit the button to unlock but did not open it. When I hit the lock on the key the cars horn made two quick blows and light flashed. Once I closed the truck it set itself then.
Sounds like the systems is reading the door ajar.

There is probably a little button near the door hinges that the door panel depresses when you close the door. At least thats how it is on most vehicles. It works the dome light and junk and lets the car know when the door is closed. Check to make sure its not broken, or popped loose from the dash.

Yeah the "door sensors" will be the same switches that causes the dome light to come on. Same thing for the trunk (and hood). Make sure they are all properly being closed and switching off.

Also I thought I remember reading that the new Fords allow user programmable locks (something to that effect regardless). That is you can program the lights to not blink, blink once, or blink twice when you lock or unlock.

If when you hit the lock button, the car fully locks around then the system should be operating fine. Unlocking the car should be once for driver side, and a quick push right after should unlock the rest of the doors (i.e. passenger side). As long as it does this it sounds like the car is fine just some settings have changed.

Usually on the PATS system the first lock will give a "silent" confirmation, that is the parking lights may or may not flash, depending on the programming. The chirp is just a "check" for the owner so if you forgot if you lovked your car or you hit lock too many times the car will let you know it has already been locked by chirping.